Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket.

(1)

HAL Id: pasteur-01132029

https://hal-riip.archives-ouvertes.fr/pasteur-01132029

Submitted on 16 Mar 2015

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Distributed under a Creative Commons Attribution| 4.0 International License

Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket.

Hanh T Pham, Max Bergoin, Peter Tijssen

To cite this version:

Hanh T Pham, Max Bergoin, Peter Tijssen. Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket.. Genome Announcements, American Society for Microbi- ology, 2013, 1 (2), pp.e0007913. �10.1128/genomeA.00079-13�. �pasteur-01132029�

(2)

Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket

Hanh T. Pham, Max Bergoin, Peter Tijssen INRS-Institut Armand-Frappier, Laval, QC, Canada

The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) mole- cule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique prop- erties of this volvovirus suggested that it belongs to a new virus family or genus.

Received1 February 2013Accepted14 February 2013 Published14 March 2013

CitationPham HT, Bergoin M, Tijssen P. 2013.Acheta domesticusvolvovirus, a novel single-stranded circular DNA virus of the house cricket. Genome Announc. 1(2):e00079-13.

doi:10.1128/genomeA.00079-13.

Address correspondence to Peter Tijssen, peter.tijssen@iaf.inrs.ca.

Cricket-breeding facilities in the United States produce billions of pet-feeder crickets annually (1, 2). The preferred house cricket,Acheta domesticus, is highly susceptible to a densovirus, Acheta domesticusdensovirus (AdDNV), which has caused severe outbreaks since September 2009 and decimated A. domesticus stocks in North America. Samples received from die-offs were invariably positive for this virus. However, some recently received samples from mass cricket die-offs in North America were negative for AdDNV.

AdDNV-negative crickets (20 g) were homogenized in 20 ml of a 3:1 mixture of phosphate-buffered saline (PBS) and carbon tet- rachloride. After low-speed centrifugation, the upper aqueous phase was passed through 0.45-nm filters and putative viruses were pelleted by centrifugation for 1.5 h at 40,000 rpm and resuspended in a small volume of Tris-EDTA (TE) buffer followed by DNase A and RNase A treatments to remove contaminating nu- cleic acids. Electron microscopy examination of a 100-fold dilu- tion of the resuspended pellet revealed highly concentrated icosa- hedral particles of about 18 nm in diameter.

DNA extracted from purified virus by the High Pure viral nu- cleic acid kit (Roche Applied Science) was resistant to restriction endonucleases and presumably single stranded. Native viral DNA was used for double-stranded DNA synthesis at 30°C by␾29 DNA polymerase (3). Amplified DNA was digested with MboI, cloned into the BamHI site of the pBluescriptSK(–) vector, and se- quenced by Sanger’s method and primer walking as described before (4). The sequences were assembled by the CAP3 program (5) and generated a 2,517-nucleotide (nt) sequence containing a single EcoRI site. PCR using native DNA and 2 sets of outward primers (with respect to the EcoRI fragment) and sequencing con- firmed the circular nature of the genome and the size of 2,517 nt.

Due to the circular (rolling) nature of the genome, the name Acheta domesticusvolvovirus (AdVVV; Volvo [Latin]⫽roll) was proposed.

Numbering of the genome started with the putative nona- nucleotide origin of replication (1-TAGTATTAC), located, as for circo- or cycloviruses (6), between the open reading frames (ORFs) with opposite orientations. Among ORF products of

⬎100 amino acids (aa), ORF1 (361 aa, starting at nt 447) and ORF4 (130 aa, starting at nt 70) were in the sense direction, whereas ORF2 (270 aa, starting at nt 2445) and the overlapping ORF3 (207 aa, starting at nt 2393) were in the antisense direction.

BLASTn failed to detect any identity to viral sequences. However, BLASTp revealed a maximum identity of about 30% between ORF2 and Rep proteins of circoviruses and cycloviruses, with a coverage of ~85% (aa 5 to 80, Viral_Rep superfamily [pfam02407], and aa 150 to 212, P-loop_NTPase [pfam00910]). The other ORFs did not have any viral identity using BLASTp.

The lack of sequence identity and the differences in genome organization and size indicated a new virus family or genus. To our knowledge, this is the first circular single-stranded DNA virus in insects that is not related to cycloviruses (7, 8), circoviruses (9–11), nanoviruses (12,13), or geminiviruses (14,15), and it may be of interest in elucidating the evolution of this rapidly expanding virus group.

Nucleotide sequence accession number.The GenBank accession number for AdVVV isKC543331.

ACKNOWLEDGMENTS

This work was supported by funds from the Natural Sciences and Engi- neering Research Council of Canada to P.T.; H.T.P. acknowledges tuition waivers at INRS.

REFERENCES

1.Szelei J, Woodring J, Goettel MS, Duke G, Jousset FX, Liu KY, Zadori Z, Li Y, Styer E, Boucias DG, Kleespies RG, Bergoin M, Tijssen P.2011.

Susceptibility of north-American and European crickets to Acheta domesticus densovirus (AdDNV) and associated epizootics. J. Invertebr. Pathol.

106:394 –399.

2.Weissman DB, Gray DA, Pham HT, Tijssen P.2012. Billions and billions sold: pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make a potential disaster. Zootaxa3504:67– 88.

3.de Vega M, Lázaro JM, Mencía M, Blanco L, Salas M. 2010. Im- provement of␾29 DNA polymerase amplification performance by fu- sion of DNA binding motifs. Proc. Natl. Acad. Sci. U. S. A. 107:

16506 –16511.

4.Tijssen P, Li Y, El-Far M, Szelei J, Letarte M, Zádori Z.2003. Organi-

Genome Announcements

March/April 2013 Volume 1 Issue 2 e00079-13 genomea.asm.org 1

(3)

zation and expression strategy of the ambisense genome of densonucleosis virus of Galleria mellonella. J. Virol.77:10357–10365.

5.Huang X, Madan A.1999. CAP3: a DNA sequence assembly program.

Genome Res.9:868 – 877.

6.Delwart E, Li L.2012. Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other rep encoding small circular ssDNA genomes. Virus Res.164:114 –121.

7.Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A.2012. Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J. Gen. Virol.93:2668 –2681.

8.Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, Collings DA, Walters M, Martin DP, Breitbart M, Varsani A.2011. Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J. Gen. Virol.92:1302–1308.

9.Dunlap DS, Ng TF, Rosario K, Barbosa JG, Greco AM, Breitbart M, Hewson I.2013. Molecular and microscopic evidence of viruses in marine copepods. Proc. Natl. Acad. Sci. U. S. A.110:1375–1380.

10. Johne R, Fernández-de-Luco D, Höfle U, Müller H.2006. Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification. J. Gen. Virol.87:1189 –1195.

11. Kapoor A, Dubovi EJ, Henriquez-Rivera JA, Lipkin WI.2012. Complete genome sequence of the first canine circovirus. J. Virol.86:7018.

12. Timchenko T, Katul L, Aronson M, Vega-Arreguín JC, Ramirez BC, Vetten HJ, Gronenborn B.2006. Infectivity of nanovirus DNAs: induc- tion of disease by cloned genome components of Faba bean necrotic yel- lows virus. J. Gen. Virol.87:1735–1743.

13. Timchenko T, Katul L, Sano Y, de Kouchkovsky F, Vetten HJ, Gronen- born B.2000. The master rep concept in nanovirus replication: identifi- cation of missing genome components and potential for natural genetic reassortment. Virology274:189 –195.

14. Buchmann RC, Asad S, Wolf JN, Mohannath G, Bisaro DM. 2009.

Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J. Virol.83:

5005–5013.

15. Martin DP, Lefeuvre P, Varsani A, Hoareau M, Semegni JY, Dijoux B, Vincent C, Reynaud B, Lett JM.2011. Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologi- cally important intra-genome interaction networks. PLoS Pathog.

7:e1002203. doi:10.1371/journal.ppat.1002203.

Pham et al.

Genome Announcements

2 genomea.asm.org March/April 2013 Volume 1 Issue 2 e00079-13